I moved your post to here.
First I should note microSD cards if you are using one with an adapter are known to cause trouble, it might not happen but if you are using an original EZ4 that normally uses miniSD try to pick one of those up.
Files..... technically it only needs a saver folder which the EZ4client should make but
ezfla_up.bin - this is the loader and if you have one of these on the root (as in just the drive- h:\\ezfla_up.bin for instance) and hold R when booting up it will flash that to the EZ4 onboard memory. You mainly do this when changing loader (not something most do after the initial update) or changing the skin (the skinning tools with make a new ezfla_up.bin file). Once it has been updated you can delete it if you want.
After this you can put roms wherever you like up to FAT16 limits (8 directories and about 255 characters if memory servers but that is quite ridiculous and nobody goes that high) and additionally only 80 files per folder if you plan on looking at it on the EZ4 (you can just stick the files in another directory)
saver will be made by the client but you can make it instead if you like. The files in here will need to be named the same as the rom but with a .sav extension- tetris.gba wherever it might be on the cart will have a file in the saver folder called tetris.sav (not all flash cards do it this way but the EZ4 does).
Assuming you picked up
http://filetrip.net/f4753-EZ4-Client-2009-04-03.html then only the ezfla_up.bin needs to be on the card. Everything else is part of the PC side software save for some of the .sav files which are workarounds for some DS games and dldi.bin in the HOMEBREW AND DLDI directory which is a piece of DS homebrew you can use to patch DLDI capable homebrew software (nothing save for a save grabbing tool on the GBA used DLDI though)
Some stick the software on the card as well to save hassle should they be on another machine but that is up to you.